The input shaft bearing (clutch side) could be bad or it could be the mainshaft bearing on the opposite side of the mainshaft (axle side).
I replaced the mainshaft bearing. I didn't need to press it off because it was stuck in the housing. I needed to use a slide hammer to pull the bearing out of the housing. The new bearing slid onto the mainshaft without pressing it on. Luckily, the new bearing was exactly the same height as the old one so I ddin't need to use a new shim. I just used the one that was there.
If your input shaft bearing is bad, it will need to be pulled out of the clutch side housing with a slide hammer. I didn't replace any of the other bearings in my VX tranny and have not had any problems in the past 45,000 miles.
There is no gasket on the halves of the tranny housing. It is sealed with Honda bond or any other decent sealant. I used the Honda bond just to be sure it worked.
The hardest part is getting the tranny off the engine. It's easier to do when the engine is removed from the car. I was able to do it by myself with engine still in the car with a transmission jack and 6 ton jack stands from Harbor Freight. It's also difficult to match up the splines on the shaft with the clutch also when working alone reinstalling the tranny to the engine. It's also a challenge to open and then close the tranny case. You'll see.
Try this repair only if you are willing to get another tranny in case you make a critical mistake. Luckily I didn't make one but it was close a couple of times.
Thanks a lot. Luckily, I have a neighbor who seems to know what he's doing. He just built an Integra motor and swapped it into an '86 CRX Si, and he rebuilt the CRX's manual tranny. The questions I asked actually came from him... I don't know much about transmissions. I hope to have him do the job, and learn a bit in the process.
If anything comes up that you don't understand, let me know and I'll try to help you figure it out. Go to Honda-tech.com and search for input shaft bearing. There's a very good write up on this you can also find if you search by my registered name on Honda-tech which is also jadziasman.